diff --git a/README.md b/README.md
index f72e8f3f0f656ef6d4b088dd7e9372b0145355cb..7f5cdff72f74bb29a42ae13e4e33ccb49f5fce12 100644
--- a/README.md
+++ b/README.md
@@ -11,6 +11,8 @@
- [x] gZip (zLib, huffman deflate combination)
- [ ] Save all different results at different settings, use different `Compression strategy`
- [ ] bzip2
+ - [ ] LZMA (7-zip)
+ - [ ] Different presets and `extreme` preset http://www.manpagez.com/man/1/lzma/
- [ ] deflate
- [ ] *B3D cuda library*
- [ ] Look at *Image difference*
@@ -60,4 +62,4 @@ Later on, we can extend our program to handle more things from the file, like:
## Image difference
- Find difference between included images.
- Plot those differences and find out if certain images aren't same, just positioned little bit differently
-- *Pattern matching* - Find if there are some patterns in image sets.
\ No newline at end of file
+- *Pattern matching* - Find if there are some patterns in image sets.
diff --git a/czi-format/czi-parser/CMakeLists.txt b/czi-format/czi-parser/CMakeLists.txt
index d3d9d45051d2a7587b57226aa8584fc4fdbb8e0c..d7f9c1f18f85fda19a2e51c970f030d3411f7e8d 100644
--- a/czi-format/czi-parser/CMakeLists.txt
+++ b/czi-format/czi-parser/CMakeLists.txt
@@ -15,13 +15,27 @@ find_package(Boost REQUIRED COMPONENTS filesystem locale)
if(Boost_FOUND)
include_directories(${Boost_INCLUDE_DIRS})
target_link_libraries(czi-parser ${Boost_LIBRARIES})
+ message("LINKED BOOST")
endif()
find_package (Threads)
target_link_libraries (czi-parser ${CMAKE_THREAD_LIBS_INIT})
find_package(ZLIB)
+if(ZLIB_FOUND)
target_link_libraries(czi-parser ${ZLIB_LIBRARIES})
+message("LINKED ZLIB")
+endif(ZLIB_FOUND)
+
+
+
+
+find_package(LibLZMA)
+if (LIBLZMA_FOUND)
+ include_directories(${LIBLZMA_INCLUDE_DIRS})
+ target_link_libraries(czi-parser ${LIBLZMA_LIBRARIES})
+ message("LINKED LIBLZMA")
+endif()
set(CPACK_PROJECT_NAME ${PROJECT_NAME})
set(CPACK_PROJECT_VERSION ${PROJECT_VERSION})
diff --git a/czi-format/czi-parser/compression/compressors.h b/czi-format/czi-parser/compression/compressors.h
index cb4488dd26313f3b69975da35221a17a5e4230cb..bcc57924ec745936e817853b063fe82ae7f9adf1 100644
--- a/czi-format/czi-parser/compression/compressors.h
+++ b/czi-format/czi-parser/compression/compressors.h
@@ -8,11 +8,23 @@ namespace library_zlib
#include <zlib.h>
};
+namespace library_lzma
+{
+#include <lzma.h>
+};
+
enum CompressionMethod
{
CompressionMethod_RLE,
CompressionMethod_LZ,
- CompressionMethod_GZIP
+ CompressionMethod_GZIP,
+ CompressionMethod_LZMA,
+};
+
+struct CompressionSettings
+{
+ size_t lzmaPreset = LZMA_PRESET_DEFAULT; //LZMA_PRESET_EXTREME;
+ bool lzmaExtreme = false;
};
struct CompressionResult
@@ -48,7 +60,7 @@ inline float compression_ratio(float uncompressedSize, float compressedSize)
return (uncompressedSize / compressedSize);
}
-ByteArray gzip_encode(const std::vector<byte> &data)
+ByteArray gzip_encode(const std::vector<byte> &data, CompressionSettings settings)
{
size_t compressedSize = library_zlib::compressBound(data.size());
ByteArray compressedBuffer;
@@ -80,6 +92,48 @@ ByteArray gzip_encode(const std::vector<byte> &data)
return actualCompressedData;
}
+ByteArray lzma_encode(const std::vector<byte> &data, CompressionSettings settings)
+{
+ size_t maximumSize = library_lzma::lzma_stream_buffer_bound(data.size());
+ ByteArray buffer;
+ buffer.resize(maximumSize);
+ size_t finalSize = 0;
+ auto compressionResult = library_lzma::lzma_easy_buffer_encode(settings.lzmaPreset, library_lzma::LZMA_CHECK_NONE,
+ nullptr, data.data(), data.size(),
+ buffer.data(), &finalSize, maximumSize);
+ switch (compressionResult)
+ {
+ case library_lzma::LZMA_MEM_ERROR:
+ printf(RED "Unable to allocate memory!\n" RESET);
+ break;
+ case library_lzma::LZMA_MEMLIMIT_ERROR:
+ printf(RED "Memory limit was reached!\n" RESET);
+ break;
+ case library_lzma::LZMA_BUF_ERROR:
+ printf(RED "Cannot consume input buffer!\n" RESET);
+ break;
+ case library_lzma::LZMA_PROG_ERROR:
+ printf(RED "Wrong arguments!\n" RESET);
+ break;
+ // To make GCC with -Wall happy.
+ case library_lzma::LZMA_OK:
+ case library_lzma::LZMA_STREAM_END:
+ case library_lzma::LZMA_NO_CHECK:
+ case library_lzma::LZMA_UNSUPPORTED_CHECK:
+ case library_lzma::LZMA_GET_CHECK:
+ case library_lzma::LZMA_FORMAT_ERROR:
+ case library_lzma::LZMA_OPTIONS_ERROR:
+ case library_lzma::LZMA_DATA_ERROR:
+ break;
+ }
+ always_assert(compressionResult == library_lzma::LZMA_OK);
+
+ ByteArray result(buffer.begin(), buffer.begin() + finalSize);
+ always_assert(result.size() == finalSize);
+
+ return result;
+}
+
// Run-Length encode bytes and return compressed bytes.
std::vector<byte> rle_encode(const std::vector<byte> &bytes)
{
@@ -328,7 +382,7 @@ void comp_test()
always_assert(same && "Error in compression!");
}
-CompressionResult test_compression_method(const ByteArray &data, CompressionMethod method)
+CompressionResult test_compression_method(const ByteArray &data, CompressionMethod method, CompressionSettings settings)
{
ByteArray compressedData;
switch (method)
@@ -340,7 +394,10 @@ CompressionResult test_compression_method(const ByteArray &data, CompressionMeth
compressedData = lz_encode(data);
break;
case CompressionMethod_GZIP:
- compressedData = gzip_encode(data);
+ compressedData = gzip_encode(data, settings);
+ break;
+ case CompressionMethod_LZMA:
+ compressedData = lzma_encode(data, settings);
break;
default:
INVALID_CASE;
diff --git a/czi-format/czi-parser/czi_file.cpp b/czi-format/czi-parser/czi_file.cpp
index 40e95c07425c305eec2a6009b88dc1ba03a8cede..8380d9fed614c5e92bc1a9a22fdd770972d10dbb 100644
--- a/czi-format/czi-parser/czi_file.cpp
+++ b/czi-format/czi-parser/czi_file.cpp
@@ -423,6 +423,9 @@ void CziFile::test_compression(CompressionMethod method, bool verbose) const
case CompressionMethod_GZIP:
printf("Selected compression: GZIP (zlib)\n");
break;
+ case CompressionMethod_LZMA:
+ printf("Selected compression: LZMA (2?)\n");
+ break;
default:
INVALID_CASE;
return;
@@ -431,13 +434,15 @@ void CziFile::test_compression(CompressionMethod method, bool verbose) const
CompressionResult overallN;
CompressionResult overallZ;
+ //TODO: Use settings.
+ CompressionSettings settings;
for (size_t i = 0; i < subBlockDirectory.entries.size(); i++)
{
auto data = get_image_data(i, false);
auto dataZ = get_image_data(i, true);
- CompressionResult nResult = test_compression_method(data, method);
- CompressionResult zResult = test_compression_method(dataZ, method);
+ CompressionResult nResult = test_compression_method(data, method, settings);
+ CompressionResult zResult = test_compression_method(dataZ, method, settings);
overallN.compressionRatio += nResult.compressionRatio;
overallZ.compressionRatio += zResult.compressionRatio;
diff --git a/czi-format/czi-parser/main.cpp b/czi-format/czi-parser/main.cpp
index e40c3368a177d2fed85fb9c2d72f9ffaf5b27509..3f1907161522da9218ee3ea23f88276e29f65755 100644
--- a/czi-format/czi-parser/main.cpp
+++ b/czi-format/czi-parser/main.cpp
@@ -24,6 +24,7 @@ int main(int argc, char **argv)
args::Flag rleCompressionOption(compressionGroup, "RLE", "RLE compression", {"rle"});
args::Flag lzCompressionOption(compressionGroup, "LZ", "LZ compression", {"lz"});
args::Flag gzipCompressionOption(compressionGroup, "GZIP", "GZIP (zlib) compression", {"gzip"});
+ args::Flag lzmaCompressionOption(compressionGroup, "LZMA", "LZMA (2?) compression", {"lzma"});
try
{
@@ -58,6 +59,8 @@ int main(int argc, char **argv)
cm = CompressionMethod_LZ;
else if (gzipCompressionOption)
cm = CompressionMethod_GZIP;
+ else if (lzmaCompressionOption)
+ cm = CompressionMethod_LZMA;
parsedFile.test_compression(cm, verboseOption.Matched());
}